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Aim: East Asia exhibits complex geomorphological and climatic characteristics. The aim of this study was to test whether the so‐called three‐step landforms of China, together with the East China Sea (ECS), have acted to shape specific phylogeographical patterns and affected the biogeographical history of the species belonging to the East Asian Flora. Location: China and Japan. Taxon: Kerria japonica (L.) DC. Methods: Three chloroplast DNA regions and 15 nuclear microsatellite (nSSR) loci were sequenced and genotyped in 576/450 individuals of K. japonica. Phylogeographical analyses were performed to assess the genetic structure, historical gene flow and demographical history of these individuals, and climatic factors were examined to determine their effects on phylogeographical breaks. Furthermore, time‐calibrated phylogenetic trees and ancestral range reconstruction were used to infer the biogeographical history of K. japonica. Potential habitats at present and during the last glacial maximum (LGM) were identified using ecological niche modelling. Results: Distinct phylogeographical breaks were found across the ECS and along the boundary of the three‐step landforms of China. Low historical gene flow and significant climatic differences were detected in each pair of adjacent regions. The results of molecular dating and ancestral range reconstruction indicated that K. japonica originated in North America during the mid‐Miocene (14.76 Ma), and intra‐specific diversification began in the late Miocene (7.78 Ma). Compared to the relatively stable distribution range of Chinese populations, Japanese populations experienced range expansion after the LGM in response to Quaternary climate change. Main conclusions: Kerria japonica has a complex biogeographical history, with a mid‐Miocene origin in North America and subsequent migration into East Asia via the Bering land bridge. The onset of intra‐specific diversification was probably associated with Asian monsoon intensifications, while exposure to the ECS floor facilitated the formation of the Japanese lineage in the late Miocene. The spatiotemporal population differentiation on the Chinese mainland demonstrates the significant role of biogeographical divides delineated by the three‐step landforms of China and provides clues to understand the floristic regionalization and evolutionary history of plant diversity in East Asia, especially with respect to the Hengduan Mountains, Central China and East China. [ABSTRACT FROM AUTHOR]

[Display omitted] • The "ampliative" Spiraea japonica complex was put forward. • Phylogeographical pattern is related to the regionalization of East Asian flora. • Genetic and diterpenoid alkaloids data support a transition belt in central China. • Diversification and demographic dynamics were shaped by the geological events. • Polyploidization contributed to the population expansion in east China. Each subkingdom of East Asian flora (EAF) has a unique evolutionary history, but which has rarely been described based on phylogeographic studies of EAF species. The Spiraea japonica L. complex, which is widespread in East Asia (EA), has received considerable attention because of the presence of diterpenoid alkaloids (DAs). It provides a proxy for understanding the genetic diversity and DA distribution patterns of species under various environmental conditions associated with the geological background in EA. In the present study, the plastome and chloroplast/nuclear DNA of 71 populations belonging to the S. japonica complex and its congeners were sequenced, combined with DA identification, environmental analyses, and ecological niche modelling, to investigate their phylogenetic relationships, genetic and DAs distribution patterns, biogeography, and demographic dynamics. An "ampliative" S. japonica complex was put forward, comprising all species of Sect. Calospira Ser. Japonicae , of which three evolutionary units carrying their respective unique types of DAs were identified and associated with the regionalization of EAF (referring to the Hengduan Mountains, central China, and east China). Moreover, a transition belt in central China with its biogeographic significance was revealed by genetic and DA distribution patterns from the perspective of ecological adaptation. The origin and onset differentiation of the "ampliative" S. japonica complex was estimated in the early Miocene (22.01/19.44 Ma). The formation of Japanese populations (6.75 Ma) was facilitated by the land bridge, which subsequently had a fairly stable demographic history. The populations in east China have undergone a founder effect after the Last Glacial Maximum, which may have been promoted by the expansion potential of polyploidization. Overall, the in-situ origin and diversification of the "ampliative" S. japonica complex since the early Miocene is a vertical section of the formation and development of modern EAF and was shaped by the geological history of each subkingdom. [ABSTRACT FROM AUTHOR]